SF-Assemblin genes in Paramecium: phylogeny and phenotypes of RNAi silencing on the ciliary-striated rootlets and surface organization

Ashikun Nabi; Junji Yano; Megan S Valentine; Tyler Picariello; Judith L Van Houten

doi:10.1186/s13630-019-0062-y

SF-Assemblin genes in Paramecium: phylogeny and phenotypes of RNAi silencing on the ciliary-striated rootlets and surface organization

Cilia. 2019 Oct 29:8:2. doi: 10.1186/s13630-019-0062-y. eCollection 2019.

Authors

Ashikun Nabi^{1

2}, Junji Yano¹, Megan S Valentine³, Tyler Picariello⁴, Judith L Van Houten¹

Affiliations

¹ 1University of Vermont, Burlington, VT 05405 USA.
² 4Present Address: Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511 USA.
³ 2State University of New York at Plattsburgh, Plattsburgh, NY 12901 USA.
⁴ 3University of Massachusetts Medical School, Worcester, MA 01655 USA.

Abstract

Background: Cilia emanate from basal bodies just underneath the cell membrane. Basal bodies must withstand torque from the ciliary beat and be appropriately spaced for cilia to beat in metachronal waves. Basal body rootlets provide stability for motile cilia. Paramecium has three. Our focus is on the largest one, the striated rootlet (SR). Paramecium basal bodies align in straight rows. Previously we found a potential role for the SR in this alignment. Here we present a phylogeny of the Paramecium homologs of the SF-Assemblin gene of the SR of Chlamydomonas, and the organization of these genes. We describe the phenotypes from RNA interference (RNAi) silencing of genes and gene groups.

Methods: Phenotypes of the RNAi depletions were characterized by immunofluorescence (IF), electron microscopy, and mass spectrometry.

Results: We found 30 genes for Paramecium SF-Assemblin homologs (SFA) organized into 13 Paralog Groups (further categorized in five Structural Groups). Representatives of Paralog Groups were found in the SRs. Silencing the transcripts of any of the Structural Groups correlates with misaligned rows of basal bodies, SRs, and cortical units. The silencing of Structural Groups was key and gave us the ability to systematically disrupt SR structures and cell surface organization.

Conclusions: Silencing of SFA genes and Paralog Groups shows no effects on the SR or the cell surface organization. Silencing of the larger Structural Groups has an enormous impact on rows of basal bodies, SRs and cortical units, and SR striations, and length. Misaligned basal bodies have cilia causing the cells to swim in abnormal paths.

Keywords: Basal body; Cilia; RNAi; Striated rootlet.

Grants and funding

P20 GM103449/GM/NIGMS NIH HHS/United States